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- PDB-3jcs: 2.8 Angstrom cryo-EM structure of the large ribosomal subunit fro... -

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Entry
Database: PDB / ID: 3jcs
Title2.8 Angstrom cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania
Components
  • (26S delta ribosomal ...) x 2
  • (ribosomal protein ...) x 40
  • 26S alpha ribosomal RNA
  • 26S epsilon ribosomal RNA
  • 26S gamma ribosomal RNA
  • 26S zeta ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Leishmania donovani / the large ribosomal subunit / eukaryotic parasite
Function / homology
Function and homology information


maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding ...maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / 60S ribosomal protein L35 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L37ae / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal L37ae protein family / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L35A superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14, KOW motif / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L37ae/L37e / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L7Ae/L8/Nhp2 family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L7a / 60S ribosomal protein L28, putative ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L7a / 60S ribosomal protein L28, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L36, Putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L32 / 60S ribosomal protein L37a / 60S ribosomal protein L11 (L5, L16) / 40S ribosomal protein L14, putative / 60S ribosomal protein L17, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L35, putative / Ribosomal protein L1a, putative / Ribosomal protein L15 / Ribosomal L27e family protein / Ribosomal protein L37 / Ribosomal protein L35Ae family protein / 60S ribosomal protein L21, putative / 60S ribosomal protein L30 / 60S ribosomal protein L18a / 60S ribosomal protein L5, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL34 / 60S ribosomal protein L18, putative / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsShalev-Benami, M. / Zhang, Y. / Matzov, D. / Halfon, Y. / Zackay, A. / Rozenberg, H. / Zimmerman, E. / Bashan, A. / Jaffe, C.L. / Yonath, A. / Skiniotis, G.
CitationJournal: Cell Rep / Year: 2016
Title: 2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania.
Authors: Moran Shalev-Benami / Yan Zhang / Donna Matzov / Yehuda Halfon / Arie Zackay / Haim Rozenberg / Ella Zimmerman / Anat Bashan / Charles L Jaffe / Ada Yonath / Georgios Skiniotis /
Abstract: Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, ...Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
1: 26S alpha ribosomal RNA
2: 26S delta ribosomal RNA
3: 26S gamma ribosomal RNA
4: 26S delta ribosomal RNA
5: 26S epsilon ribosomal RNA
6: 26S zeta ribosomal RNA
7: 5.8S ribosomal RNA
8: 5S ribosomal RNA
A: ribosomal protein L2
B: ribosomal protein L3
C: ribosomal protein L4
D: ribosomal protein L5
E: ribosomal protein L6
F: ribosomal protein L6e
G: ribosomal protein L8e
H: ribosomal protein L13
I: ribosomal protein L13e
J: ribosomal protein L14
K: ribosomal protein L14e
L: ribosomal protein L15
M: ribosomal protein L15e
N: ribosomal protein L16
O: ribosomal protein L18
P: ribosomal protein L18e
Q: ribosomal protein L19e
R: ribosomal protein L20e
S: ribosomal protein L21e
T: ribosomal protein L22
U: ribosomal protein L22e
V: ribosomal protein L23
W: ribosomal protein L24
X: ribosomal protein L24e
Y: ribosomal protein L27e
Z: ribosomal protein L28e
a: ribosomal protein L29
b: ribosomal protein L29e
c: ribosomal protein L30
d: ribosomal protein L30e
e: ribosomal protein L31e
f: ribosomal protein L32e
g: ribosomal protein L33e
h: ribosomal protein L34e
i: ribosomal protein L36e
j: ribosomal protein L37e
k: ribosomal protein L38e
l: ribosomal protein L39e
m: ribosomal protein L43e
n: ribosomal protein L44e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,170,515157
Polymers2,167,86648
Non-polymers2,649109
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 6 types, 6 molecules 135678

#1: RNA chain 26S alpha ribosomal RNA


Mass: 576874.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#3: RNA chain 26S gamma ribosomal RNA


Mass: 68191.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#5: RNA chain 26S epsilon ribosomal RNA


Mass: 42869.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#6: RNA chain 26S zeta ribosomal RNA


Mass: 24254.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#7: RNA chain 5.8S ribosomal RNA /


Mass: 54961.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#8: RNA chain 5S ribosomal RNA /


Mass: 38840.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)

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26S delta ribosomal ... , 2 types, 2 molecules 24

#2: RNA chain 26S delta ribosomal RNA


Mass: 492600.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#4: RNA chain 26S delta ribosomal RNA


Mass: 59130.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)

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Ribosomal protein ... , 40 types, 40 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#9: Protein ribosomal protein L2 /


Mass: 28331.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#10: Protein ribosomal protein L3 /


Mass: 47672.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#11: Protein ribosomal protein L4 / 60S ribosomal protein L4


Mass: 41228.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BKR3
#12: Protein ribosomal protein L5 / 60S ribosomal protein L5


Mass: 21710.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFL1
#13: Protein ribosomal protein L6 /


Mass: 21567.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFB5
#14: Protein ribosomal protein L6e / Ribosome


Mass: 21208.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#15: Protein ribosomal protein L8e / Ribosome


Mass: 39175.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B949
#16: Protein ribosomal protein L13 / 60S ribosomal protein L13


Mass: 25477.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#17: Protein ribosomal protein L13e / Ribosome


Mass: 24802.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#18: Protein ribosomal protein L14 /


Mass: 14982.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ4
#19: Protein ribosomal protein L14e / Ribosome


Mass: 26054.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BG02
#20: Protein ribosomal protein L15 /


Mass: 16165.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSQ2
#21: Protein ribosomal protein L15e / Ribosome


Mass: 24497.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BMB4
#22: Protein ribosomal protein L16 /


Mass: 24607.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B840
#23: Protein ribosomal protein L18 /


Mass: 34100.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BS61
#24: Protein ribosomal protein L18e / Ribosome


Mass: 22071.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUI1
#25: Protein ribosomal protein L19e / Ribosome


Mass: 28142.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B8Q2
#26: Protein ribosomal protein L20e / Ribosome


Mass: 20834.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRT7
#27: Protein ribosomal protein L21e / Ribosome


Mass: 18059.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRE2
#28: Protein ribosomal protein L22 / 60S ribosomal protein L22


Mass: 19154.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BGL6
#29: Protein ribosomal protein L22e / Ribosome


Mass: 15030.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU52
#30: Protein ribosomal protein L23 /


Mass: 16389.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B8R9
#31: Protein ribosomal protein L24 /


Mass: 16217.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#32: Protein ribosomal protein L24e / Ribosome


Mass: 14622.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#33: Protein ribosomal protein L27e / Ribosome


Mass: 15455.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BP34
#34: Protein ribosomal protein L28e / Ribosome


Mass: 16409.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BAU9
#35: Protein ribosomal protein L29 /


Mass: 15232.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BIP6
#36: Protein ribosomal protein L29e / Ribosome


Mass: 8033.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BU64
#37: Protein ribosomal protein L30 /


Mass: 28929.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BI29
#38: Protein ribosomal protein L30e / Ribosome


Mass: 11400.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BRQ6
#39: Protein ribosomal protein L31e / Ribosome


Mass: 20886.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BSK4
#40: Protein ribosomal protein L32e / Ribosome


Mass: 15403.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFJ5
#41: Protein ribosomal protein L33e / Ribosome


Mass: 16492.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BR22
#42: Protein ribosomal protein L34e / Ribosome


Mass: 19307.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BUA1
#43: Protein ribosomal protein L36e / Ribosome


Mass: 12005.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BF65
#44: Protein ribosomal protein L37e / Ribosome


Mass: 9862.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BQD7, UniProt: P62885*PLUS
#45: Protein ribosomal protein L38e / Ribosome


Mass: 9479.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9B7P2
#46: Protein ribosomal protein L39e / Ribosome


Mass: 6504.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BCX6
#47: Protein ribosomal protein L43e / Ribosome


Mass: 10337.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BFK4
#48: Protein ribosomal protein L44e / Ribosome


Mass: 12302.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: E9BBL5

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Non-polymers , 2 types, 253 molecules

#49: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 109 / Source method: obtained synthetically / Formula: Mg
#50: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1The large ribosomal subunit from the eukaryotic parasite Leishmania donovaniRIBOSOME0
226S alpha ribosomal RNA1
326S beta ribosomal RNA1
426S gamma ribosomal RNA1
526S delta ribosomal RNA1
626S epsilon ribosomal RNA1
726S zeta ribosomal RNA1
Buffer solutionName: 20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT
pH: 7.6
Details: 20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 seconds on glow-discharged holey carbon grids (Quantifoil R2/2) coated with continuous thin carbon film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 7, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Calibrated magnification: 25000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1RELION3D reconstruction
2RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Maximum likelihood / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107134 / Nominal pixel size: 1 Å / Actual pixel size: 1 Å / Symmetry type: POINT
Displacement parametersBiso max: 167 Å2 / Biso mean: 39.2037 Å2 / Biso min: 2.89 Å2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms43729 73116 109 144 117098
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007125346
ELECTRON MICROSCOPYf_angle_d0.864185831
ELECTRON MICROSCOPYf_chiral_restr0.0523645
ELECTRON MICROSCOPYf_plane_restr0.00611141
ELECTRON MICROSCOPYf_dihedral_angle_d20.16467546

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